British scholar Tom Holland found himself in a firestorm—and under threat—when he raised doubts about the traditional account of the origins of Islam.

Ever since 1989, when the novelist Salman Rushdie found himself sentenced to death by Ayatollah Ruhollah Khomeini for the perceived blasphemy of “The Satanic Verses,” satirists in Europe have known that they were living on the edge of a volcano. Nervousness about mocking religious sensibilities has become more intense on the continent of Voltaire and Byron than at any time since the 18th century. That there are Muslims capable of taking murderous offense at blasphemy in a way that churches have long since outgrown is a reality that nobody who laughs at Islam can possibly forget. The cartoonists murdered Wednesday in the office of the French magazine Charlie Hebdo knew the risks they were running. That was the measure of their bravery. “What I am saying may be a bit pompous,” their editor had declared, “but I prefer to die standing than live on my knees.”

I had always admired such boldness, but I was far too pusillanimous to imagine that I might ever find myself in any danger of this sort. I was a historian, not a satirist—and, what’s more, a historian of classical antiquity. How could a book on ancient Rome offend anyone?

The answer only gradually began to dawn on me when I came to write not about Rome’s heyday but about her fall. By the 6th century A.D., the Roman Empire had been dismembered. The western half, including Italy itself, was ruled by barbarians; only the eastern half survived. In the early 7th century, that remnant was reduced, in turn, to a bleeding trunk. Provinces that had been Roman for centuries were lost for good to a new breed of imperialists: the Arabs.

How had this happened? The fall of the Roman Empire in the East seemed to me a fascinating, decisive and curiously under-discussed topic. In 2007, without really weighing up the likely consequences, I decided to make it the theme of my next book.

Fools rush in where angels fear to tread. The collapse of Roman power in the Near East was the flip side of another story: the rise of Islam. The Arab armies who seized from the Romans the provinces of Palestine, Syria and Egypt were Muslim, according to traditional historiography, and had been inspired to their remarkable feats of conquest by the revelations of a prophet, Muhammad. It took me only a cursory immersion in the scholarship of the period to realize that these presumptions were (to put it mildly) widely contested.

Indeed, it was hard to think of another field of history where quite so much was up for grabs. Questions fundamental to Islam’s traditional understanding of itself turned out to defy consensus. Might the Arab conquerors not actually have been Muslim at all? Did the Quran, the supposed corpus of Muhammad’s revelations, in fact derive from a whole multiplicity of pre-existing sources? Was it possible that Muhammad himself, rather than coming from Mecca, had lived far to the north, in the deserts beyond Roman Palestine? The answer to all these questions, I gradually came to conclude, was yes.

For the first time, I found that writing a book about ancient history was giving me sleepless nights. That, though, was nothing compared with the nervousness I felt after receiving a second commission: to make a film about the origins of Islam. It came from Channel 4, a TV station that had been set up in the U.K. back in the 1980s with a publicly funded remit to serve as the BBC’s naughty younger brother. Ever since, no Christmas or Easter has been complete in Britain without a documentary in its schedule questioning the historicity of the Bible.

Never before, though, had it—or, indeed, any other British TV channel—aired a documentary questioning the basis of what most Muslims believed about the origins of their faith. I still remember a feeling of almost physical panic as I stood on the battlements of an abandoned Roman city in the Negev Desert and raised the possibility, on camera, that Muhammad might not have come from Mecca. The director, the brilliant and award-winning filmmaker Kevin Sim, had aimed to make me and my anxieties about what I was doing a part of the film, and he more than succeeded. There is barely a shot in the documentary in which I do not look mildly terrified.

Nevertheless, by the time the program finally aired in late August 2012, I had come to feel more sanguine about its prospects. My book had come out four months before, and I had not felt threatened in any way. Reviews had been mixed, which was no surprise considering how controversial the subject matter was: Some were adulatory, some vituperative. Muslim critics, without exception, had hated it. None, though, to my relief, had disputed my right to subject the origins of Islam to historical inquiry and to publish my conclusions. For that reason, as I looked ahead to the airing of the documentary, I felt tolerably confident that no one would get too upset.

It didn’t take long for me to realize my mistake. Just a few minutes into the broadcast, my Twitter stream was going up in smoke. By the time the show ended, the death threats were coming in thick and fast—and not just against me but against my family as well. Channel 4 was also deluged with protests. A private screening scheduled for assorted movers and shakers had to be canceled after the police warned that they couldn’t guarantee the security of those attending the event. Because many of the invitees had been journalists, this naturally gave the controversy a new lease of life.

Two weeks later, I was still fielding death threats from Muslims convinced that the only plausible explanation for my having made the film was that I was in the pay of Mossad or the CIA or both. The most chilling moment of all came when Press TV, a propaganda arm of the Iranian government, aired a documentary leveling pretty much that accusation. It was the one time that I seriously imagined I might end up as the new Salman Rushdie.

Gradually, though, the protests faded away, as storm clouds of outrage tend to do. My wife and children put away the emergency call devices given to them by the police, and we all breathed a collective sigh of relief. Over the succeeding months, I was invited to address various public meetings hosted by Muslim organizations, and the attendees, though rarely enthusiastic about my arguments, gave me a perfectly amicable hearing.

At a conference organized by Oxford University to discuss my book and film, I was asked what lessons I had learned. The chief one, I answered, was that the freedom to write history without intimidation was no longer something that I took for granted. But I also had learned that it was possible, when my work came under attack, to defend it without yielding to threats.

I have not changed my mind. My experience did not remotely approach the horror of the massacre at Charlie Hebdo, but just as its staff were willing to die in defense of what they saw as the legacy of Diderot, so should historians be conscious of what is at stake in defense of the legacy of Gibbon. Compared with satirists and polemicists, we stand a good way back from the front line, but none of us should be in any doubt that we are in the same fight.

—Mr. Holland is the author of “Rubicon: The Last Years of the Roman Republic” and “In the Shadow of the Sword: The Birth of Islam and the Rise of the Global Arab Empire.” His new translation of “The Histories” of Herodotus is published by Penguin Classics. His documentary, “Islam: The Untold Story,” is available online in the U.K.

Corrections & Amplifications

An earlier version of this article incorrectly said the author had raised the possibility, on camera, that Muhammad might not have come to Mecca.